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CO-removed state of the active site of vanadium nitrogenase VFe protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.576 α = 83.99 b = 80.027 β = 72.48 c = 107.2 γ = 75.03
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9116 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.05 46.66 94.1 0.999 10.2 7 1016322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 0.449
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6FEA 1.05 46.66 1011232 5039 94.09 0.1208 0.1208 0.1207 0.141 0.1409 RANDOM 13.231
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.21 0.18 0.39 0.55 -0.15 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_1_deg 19.986 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 12.448 r_rigid_bond_restr 4.388 r_angle_refined_deg 3.116 r_angle_other_deg 1.864 r_chiral_restr 0.495 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_1_deg 19.986 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 12.448 r_rigid_bond_restr 4.388 r_angle_refined_deg 3.116 r_angle_other_deg 1.864 r_chiral_restr 0.495 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16711 Nucleic Acid Atoms Solvent Atoms 2678 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing